The multitudes of scooters that appeared on San Francisco’s sidewalks in late March could vanish for most of June as the city begins the process of issuing permits to motorized scooter rental companies, authorities announced Thursday.

In a move sure to upset customers and the three companies renting scooters, the city will require Bird, LimeBike and Spin to stop operations on city sidewalks on June 4 and not resume rentals until permits are issued.

“As of June 4, they have to be off of the city streets (and sidewalks),” City Attorney Dennis Herrera said. “In the event they are not taken off the streets the (Municipal Transportation Agency) will take that behavior into account, and I will reserve the right to do anything legally to make sure the law is enforced.”

Rachel Starr, a spokeswoman for Spin, said the company would remove its scooters and is working on its application.

“We are excited to apply for a permit and will comply with the city’s request that all electric scooters be removed by June 4,” the firm said in a statement.

Bird spokesman Kenneth Baer said: “We look forward to working closely with the SFMTA to obtain a permit. In just a short time, tens of thousands of San Franciscans have ridden more than 100,000 miles on Birds. The demand for a way to get around San Francisco that does not add to congestion or carbon emissions is clear, and we look forward to meeting it in the days to come.”

Companies will be fined $100 a day, plus fees, for each scooter left in a public right of way after June 4.

Applications for permits, which are limited to five companies, were available beginning Thursday afternoon.

“San Francisco supports transportation innovation, but it cannot come at the price of public safety,” Herrera said earlier in a written statement. “ We can have innovation but it must keep our sidewalks safe and accessible for all pedestrians,” he said.

Rental scooters have been a source of controversy since they suddenly appeared on sidewalks by the hundreds at the end of March. In their short time in the city, the two-wheelers have become a divisive issue, drawing passionate fans and enraged foes.

Riders say the scooters, which rent for $1 plus 15 cents per minute, and can travel up to 15 mph, provide an inexpensive, fast and fun way to make short trips around the city, whether between BART and work, to lunch or to attend meetings.

Critics, including advocates for pedestrians, seniors and people with disabilities, along with some merchants, complain that they are often parked blocking sidewalks, ramps and bus stops. Some scooter users ride on sidewalks and without helmets or drivers licenses, in violation of state law.

City officials have taken a middle ground but a hard line, saying they welcome scooters and consider them a valuable way to get around the city, as long as users and companies obey the law and maintain a sense of decorum.

“We support the spirit of innovation that the scooter companies bring to creating sustainable options for getting around,” said Ed Reiskin, transportation director for the San Francisco Municipal Transportation Agency, “and we will be holding them to high standards in the public interest.”

After being flooded with complaints, Public Works officials confiscated hundreds of scooters that were blocking sidewalks. The Board of Supervisors granted the SFMTA the power to regulate and require permits for rental scooters, and the city attorney issued a cease-and-desist order banning the rental companies from operating illegally.

The permit process adopted by the SFMTA allows for a one-year trial permit program that allows no more than five motorized scooter rental companies to operate in the city and places a cap on the total number of scooters: 1,250 during the first six months, possibly rising to 2,500 during the second six.

As part of their permit applications, companies must show how they will keep the sidewalks clear of scooters, provide insurance, offer plans for low-income riders, provide trip data to the SFMTA, and protect the privacy of scooter renters and their mobile phone data.

“This program is a strong step forward,” Herrera said. “It provides the framework to ensure that companies operating in the public right of way are doing so lawfully and are accountable.”

Michael Cabanatuan has covered all things transportation for the San Francisco Chronicle — from BART strikes, acrobatic bridge construction and dark dirty tunnel excavations to the surging ridership on public transportation and the increasing conflict as cars, bikes and pedestrians struggle to coexist on the streets. He’s ridden high-speed trains in Japan, walked in BART’s Transbay Tube and driven to King City at 55 mph to test fuel efficiency.

He joined The Chronicle as a suburban reporter and deputy bureau chief in Contra Costa County, and has also covered the general assignment beat. In addition to transportation, Michael covers a variety of Bay Area news, including breaking news events. He’s been tear-gassed covering demonstrations in Oakland and exposed to nude protesters in the Castro District. Michael is also a regular contributor to the City Insider column and blog.